[gmx-users] Gromacs with Plumed

[Szilárd Páll]

Hi,

The discussion will continue on gmx-developers, those interested in
following it should head there (subscribe or read it here
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2017-March/009540.html)


On Fri, Mar 3, 2017 at 9:36 AM, Giovanni Bussi <bussi at sissa.it> wrote:
> Hi,
>
> thanks Szilárd for the comment.
>
> About changing the version string, which would be the right place to do it
> in the code?

This however concerns users too, so let me repeat what I wrote on the
other list:

Firstly, regarding the version info: all you need to do is to set e.g.
GMX_VERSION_SUFFIX='-PLUMED-2.0' in cmake/gmxVersionInfo.cmake to get
a version string that looks like this: "2016.2-PLUMED-2.0.

Until this is done by the PLUMED installer/patch, I would strongly
recommend users and especially admins doing shared installations that,
for the sake of reproducibility add a version suffix in the above
suggested manner so that
gmx -version
mdrun_mpi -version
reflects the code that the respective tool was compiled from!

Cheers,
--
Szilárd


> About the last point, do you mean that we should try to put our code into
> gromacs main trunk? This would be very nice for us (plumed developers), and
> we discussed several times about this. Do you think it would be feasible?
> Are there clear guidelines about what should be included, how, and where in
> the code (e.g. a developer manual)?
>
> Honestly, the current patch is very dirty (we use some global variables
> here and there to avoid modifying function declarations), but with some
> help we could perhaps make it clean and try to contribute it.
>
> Thanks!
>
> Giovanni
>
>
>
> On Thu, Mar 2, 2017 at 3:43 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>
>> Hi,
>>
>> I'd recommend keeping a vanilla/untainted GROMACS installation
>> available to users at all times. No matter how much awareness there is
>> about issues or unwanted code interaction, as long as a user is not
>> running an official GROMACS release, they can and should not claim
>> (e.g. in a publication) that they used "GROMACS vX.Y". This is not
>> just nitpicking, but a matter of scientific reproducibility.
>>
>> I hope that PLUMED patching also changes the version string not just
>> the code so installations from "patched" source do not claim to be
>> vanilla, official GROMACS. Can you or someone else aware confirm that?
>>
>>
>> On a side-note, the uncomfortable side-effect of the patch-based
>> software distribution model would of course be easy to solve if thin
>> API abstractions were designed and submitted upstream in the main
>> GROMACS source.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>> On Thu, Mar 2, 2017 at 9:09 AM, Åke Sandgren <ake.sandgren at hpc2n.umu.se>
>> wrote:
>> > Hi!
>> >
>> > Are there any known drawbacks to building Gromacs with Plumed?
>> >
>> > I'm mainly talking about Gromacs 2016 and later, using PLumed 2.3.0,
>> > both if there are problems with any version combination i'd like to know
>> > that too.
>> >
>> > I.e., will it cause problems for non-plumed runs, will gromacs behave
>> > identical to a non-plumed build when not using plumed in the
>> > plumed-build, etc.?
>> >
>> > Having just a single build makes my life easier :-)
>> >
>> > --
>> > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
>> > Internet: ake at hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
>> > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
>> > --
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>
>
>
> --
> Giovanni Bussi
> Scuola Internazionale Superiore di Studi Avanzati - SISSA
> via Bonomea 265, 34136 Trieste, Italy
> email: bussi at sissa.it
> web:   http://people.sissa.it/~bussi
>           http://srnas.sissa.it
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